Linux y ROMS

[Mr-Ubuntu]

Hola que tal, alguien alguna vez ha trabajado con Modelos hidrodinámicos.
Estoy instalando ROMS (http://myroms.org) en un sistema Fedora Core 7.
Alguien me puede auxiliar con la instalación. ya tengo todos los paquetes necesarios, asi también instalé el compilador de Fortran (Requerido para el funcionamiento del modelo).
pero cuando compilo el archivo "./jobcomp" me aparece el siguiente error:

[root@localhost Run]# ./jobcomp
OPERATING SYSTEM IS: Linux
PROCESSOR IS: i686
cp: No existe correspondencia.
/bin/rm -rf core *.o AGRIFZOOM/AGRIF_YOURFILES/*.o *.i *.s *.f *.trace *.mod
/bin/rm -rf roms mpc cross_matrix cppcheck srcscheck checkkwds partit ncjoin ncrename ./rii_files
fpp -free -P -I../netcdf_ifc/ mpc.F > mpc.f
mpc.F(124): #warning: keyword redefined: integer
ifort -O3 -w90 -w95 -cm -72 -fno-alias -i4 -r8 -Vaxlib -o mpc mpc.f
/opt/intel/fc/10.1.018/bin/fortcom: error while loading shared libraries: libstdc++.so.5: cannot open shared object file: No such file or directory
ifort: error #10257: Fatal error in /opt/intel/fc/10.1.018/bin/fortcom, terminated by 0x7f
make: *** [mpc] Error 127
fpp -free -P -I../netcdf_ifc/ main.F | ./mpc > main.f
/bin/sh: ./mpc: No existe el fichero o el directorio
make: *** [main.o] Error 127
mv: no se puede efectuar `stat' sobre «roms»: No existe el fichero o el directorio

les agradezco..buen dia.

[AlvaroG]

Veo un par de errores.
Primero, se está quejando de que no tiene la biblioteca libstdc++.so.5
Segundo, elimina el archivo roms y después intenta acceder a él, ¡qué extraño!

Antes que nada, asegurate de instalar la biblioteca que falta, luego probá de nuevo.


Saludos.

[Mr-Ubuntu]

Ok. gracias compañero. no tenia instalada la libreria que me dices. la instalé y ya me compilò bien el ./jobcomp
estoy configurando ahora el modelo...luego te cuento.

[Mr-Ubuntu]

Hola que tal..jeje yo otra vez. ya sali del apuro de la libreria. pero ahora para correr el modelo desde matlab (que es la unica manera de correrlo) segun el manual tengo que agregar unas path's, ya las agregué pero segun el manual que para ejecutarlo desde mi versión de MatLab que es la 7.4.0 (R2007a) tengo quemodificar unas lineas al archivo:
/home/ROMS/Roms_tools/Run/start.m
-------------------------------------------------------------------------------------------------------------------------------------------------
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%
%
% Add the paths of the different toolboxes
%
% Further Information:
% http://www.brest.ird.fr/Roms_tools/
%
% This file is part of ROMSTOOLS
%
% ROMSTOOLS is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published
% by the Free Software Foundation; either version 2 of the License,
% or (at your option) any later version.
%
% ROMSTOOLS is distributed in the hope that it will be useful, but
% WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston,
% MA 02111-1307 USA
%
% Copyright (c) 2005-2006 by Patrick Marchesiello and Pierrick Penven
% e-mail:[email protected]
%
% Updated 10-Sep-2006 by Pierrick Penven
% Updated 22-Sep-2006 by Pierrick Penven (64 bits test)
% Updated 24-Oct-2006 by Pierrick Penven (mask added)
% Updated 16-jan-2007 by Pierrick Penven (quikscat added)
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%
disp(['Add the paths of the different toolboxes'])
mypath='../';
%
% ROMSTOOLS directories
%
addpath([mypath,'Aforc_NCEP'])
addpath([mypath,'Aforc_QuikSCAT'])
addpath([mypath,'Diagnostic_tools'])
addpath([mypath,'Forecast_tools'])
addpath([mypath,'Nesting_tools'])
addpath([mypath,'Preprocessing_tools'])
addpath([mypath,'Oforc_OGCM'])
addpath([mypath,'Opendap_tools'])
addpath([mypath,'Tides'])
addpath([mypath,'Visualization_tools'])
addpath([mypath,'Run/TEST_CASES'])
%
% Other software directories
%
addpath([mypath,'air_sea'])
addpath([mypath,'mask'])
addpath([mypath,'m_map'])
addpath([mypath,'netcdf_matlab'])
addpath([mypath,'netcdf_matlab/ncfiles'])
addpath([mypath,'netcdf_matlab/nctype'])
addpath([mypath,'netcdf_matlab/ncutility'])
%
% Get the path to the mexcdf (it depends on the architecture)
%
!uname -p > .mysystem
fid=fopen('.mysystem');
mysystem=fscanf(fid,'%s');
fclose(fid);
matversion=version('-release');
myversion=str2num(matversion(1:2));
!rm -f .mysystem
disp(['Arch : ',mysystem,' - Matlab version : ',matversion])
if (strcmp(mysystem(end-1:end),'64') & (myversion > 13))
disp('Use of mexnc and loaddap in 64 bits.')
addpath([mypath,'mexnc']) % 64bits version of mexnc
addpath([mypath,'Opendap_tools/FEDORA_X64']) % 64bits version of loaddap
elseif (strcmp(mysystem(end-1:end),'86') | (myversion <= 13))
disp('Use of mex60 and loaddap in 32 bits.')
addpath([mypath,'mex60']) % older version of mexcdf
addpath([mypath,'Opendap_tools/FEDORA']) % tested on matlab6 / fedora4
else
disp(['Arch : ',mysystem,...
' you should provide the paths of your own loaddap and mexcdf directories'])
end


------------------------------------------------------------------------------------------------------------------------------------------
alguien sabe que lineas debo modificar para que cargue con mi versión de MatLab.

Les agradezco mucho.. buen dia. Saludos.

[Mr-Ubuntu]

Hola que tal..jeje :-) yo otra vez. ya sali del apuro de la libreria. pero ahora para correr el modelo desde matlab (que es la unica manera de correrlo) segun el manual tengo que agregar unas path's, ya las agregué pero segun el manual que para ejecutarlo desde mi versión de MatLab que es la 7.4.0 (R2007a) tengo quemodificar unas lineas al archivo:
/home/ROMS/Roms_tools/Run/start.m
-------------------------------------------------------------------------------------------------------------------------------------------------
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%
%
% Add the paths of the different toolboxes
%
% Further Information:
% http://www.brest.ird.fr/Roms_tools/
%
% This file is part of ROMSTOOLS
%
% ROMSTOOLS is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published
% by the Free Software Foundation; either version 2 of the License,
% or (at your option) any later version.
%
% ROMSTOOLS is distributed in the hope that it will be useful, but
% WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston,
% MA 02111-1307 USA
%
% Copyright (c) 2005-2006 by Patrick Marchesiello and Pierrick Penven
% e-mail:[email protected]
%
% Updated 10-Sep-2006 by Pierrick Penven
% Updated 22-Sep-2006 by Pierrick Penven (64 bits test)
% Updated 24-Oct-2006 by Pierrick Penven (mask added)
% Updated 16-jan-2007 by Pierrick Penven (quikscat added)
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%
disp(['Add the paths of the different toolboxes'])
mypath='../';
%
% ROMSTOOLS directories
%
addpath([mypath,'Aforc_NCEP'])
addpath([mypath,'Aforc_QuikSCAT'])
addpath([mypath,'Diagnostic_tools'])
addpath([mypath,'Forecast_tools'])
addpath([mypath,'Nesting_tools'])
addpath([mypath,'Preprocessing_tools'])
addpath([mypath,'Oforc_OGCM'])
addpath([mypath,'Opendap_tools'])
addpath([mypath,'Tides'])
addpath([mypath,'Visualization_tools'])
addpath([mypath,'Run/TEST_CASES'])
%
% Other software directories
%
addpath([mypath,'air_sea'])
addpath([mypath,'mask'])
addpath([mypath,'m_map'])
addpath([mypath,'netcdf_matlab'])
addpath([mypath,'netcdf_matlab/ncfiles'])
addpath([mypath,'netcdf_matlab/nctype'])
addpath([mypath,'netcdf_matlab/ncutility'])
%
% Get the path to the mexcdf (it depends on the architecture)
%
!uname -p > .mysystem
fid=fopen('.mysystem');
mysystem=fscanf(fid,'%s');
fclose(fid);
matversion=version('-release');
myversion=str2num(matversion(1:2));
!rm -f .mysystem
disp(['Arch : ',mysystem,' - Matlab version : ',matversion])
if (strcmp(mysystem(end-1:end),'64') & (myversion > 13))
disp('Use of mexnc and loaddap in 64 bits.')
addpath([mypath,'mexnc']) % 64bits version of mexnc
addpath([mypath,'Opendap_tools/FEDORA_X64']) % 64bits version of loaddap
elseif (strcmp(mysystem(end-1:end),'86') | (myversion <= 13))
disp('Use of mex60 and loaddap in 32 bits.')
addpath([mypath,'mex60']) % older version of mexcdf
addpath([mypath,'Opendap_tools/FEDORA']) % tested on matlab6 / fedora4
else
disp(['Arch : ',mysystem,...
' you should provide the paths of your own loaddap and mexcdf directories'])
end


------------------------------------------------------------------------------------------------------------------------------------------
alguien sabe que lineas debo modificar para que cargue con mi versión de MatLab.

Les agradezco mucho.. buen dia. Saludos. :aplauso:

[Tavo-002]

Hola amigos, veo que tienen problemas compilando el roms, yo también tengo algunos problemas, podrían ayudarme?

Instale el compilador de fortran de intel para linux-64 y este es mi problema cuando ejecuto el jobcomp:

./jobcomp
OPERATING SYSTEM IS: Linux
PROCESSOR IS: x86_64
file namelist.trc.sms exists in Run directory
/bin/cp: No match.
/bin/cp: No match.
fpp: Command not found.
fpp: Command not found.
/bin/rm -rf core *.o AGRIFZOOM/AGRIF_YOURFILES/*.o *.i *.s *.f *.trace *.mod
/bin/rm -rf roms mpc cross_matrix cppcheck srcscheck checkkwds partit ncjoin ncrename ./rii_files
fpp -free -P -I../netcdf_x86_64 -IROMSFILES/AGRIF_INC mpc.F > mpc_.f
/bin/sh: fpp: not found
make: *** [mpc] Error 127
fpp: Command not found.
fpp -free -P -I../netcdf_x86_64 -IROMSFILES/AGRIF_INC main.F | ./mpc > main_.f
/bin/sh: fpp: not found
/bin/sh: ./mpc: not found
make: *** [main.o] Error 127
mv: cannot stat `roms': No such file or directory

Gracias de antemano por la ayuda que me puedan dar.

Saludos,
Tavo

[AlvaroG]

fpp: Command not found.

Creo que se refiere a esto: Intel Fortran Compiler for Linux

[Mr-Ubuntu]

Hola a todos. Aofotunadamente ya arregle el problema para mi versión de MatLab. pero ahora tengo otro problema.

--> Entro a matlab y me cambio a la ruta /home/ROMS/Roms_tools/Run

--> Desde esta ruta ejecuto la instrucción start y me muestra lo siguiente, por lo que puedo ver ya esta bien configuradas las paths de mi version de matlab.

Add the paths of the different toolboxes
Use of mex60 and loaddap in 32 bits.

--> Ahora, Cuando ejecuto la instrucción make_grid me muestra lo siguiente indicándome un error.

Making the grid: ../Run/ROMS_FILES/roms_grd.nc

Title: Benguela Test Model

Resolution: 1/3 deg

Create the grid file...
LLm = 23
MMm = 31

Fill the grid file...

Compute the metrics...
??? Error: File: subsref.m Line: 128 Column: 9
"subs" previously appeared to be used as a function or command, conflicting with its use here as the name of a variable.
A possible cause of this error is that you forgot to initialize the
variable, or you have initialized it implicitly using load or eval.


Error in ==> netcdf.subsref at 52
result = subsref(result, s);

Error in ==> get_metrics at 35
latu=nc{'lat_u'}(:);

Error in ==> make_grid at 95
[pm,pn,dndx,dmde]=get_metrics(grdname);

================================================== ===
Por lo que puedo ver (si no me falla mi ingles) en el error me dice que la variable "subs" no esta inicializada. Anexo en codigo que tengo del archivo subsref.m


function theResult = subsref(self, theStruct)

if nargin < 1, help(mfilename), return, end

if length(theStruct) < 1
result = self;
if nargout > 0
theResult = result;
else
disp(result)
end
return
end

% Quick processing.
% The NetCDF file must already be in "data" mode.

isQuick = quick(self) & ...
length(theStruct) == 1 & ...
isequal(theStruct.type, '()');

if isQuick
indices = theStruct.subs;
if ~iscell(indices), indices = {indices}; end
if (0) % Slow, but proper.
theNCid = ncid(self);
theVarid = varid(self);
theSize = ncsize(self); % Slow.
start = zeros(size(theSize));
count = zeros(size(theSize));
theAutoscaleflag = autoscale(self);
else % Fast, but very bad manners.
s = struct(self);
s = s.ncitem;
s = struct(s);
theNCid = s.itsNCid;
theVarid = s.itsVarid;
start = zeros(1, length(indices));
count = zeros(1, length(indices));
theAutoscaleflag = s.itIsAutoscaling;
end
for i = 1:length(indices)
k = indices{i};
start(i) = min(k) - 1;
count(i) = length(k);
end
[result, status] = ncmex('varget', theNCid, theVarid, ...
start, count, theAutoscaleflag);
if status >= 0
result = permute(result, length(size(result)):-1:1);
end
if nargout > 0
theResult = result;
else
disp(result)
end
return
end

% Composite-variable processing.
% We map the source-indices to the destination-indices
% for each composite-variable participant. The indices
% are in cells of cells, arranged in the same order as
% the variables, which themselves are in a cell.

theVars = var(self); % A cell.
if ~isempty(theVars)
[theSrcsubs, theDstsubs] = subs(self); % The mappings.
for j = 1:length(theSrcsubs)
siz = size(theVars{j});
src = theSrcsubs{j};
for i = 1:length(src)
if isequal(src{i}, ':') % Convert to numbers.
src{i} = 1:siz(i);
end
end
theSrcsubs{j} = src;
end
theSize = zeros(size(theDstsubs));
for j = 1:length(theDstsubs)
dst = theDstsubs{j};
for i = 1:length(dst)
theSize(i) = max(theSize(i), max(dst{i}));
end
end
theSubs = theStruct(1).subs;
if ~iscell(theSubs), theSubs = {theSubs}; end
isColon = isequal(theSubs{end}, ':');
if isColon, s = ':'; else, s = 1; end
while length(theSubs) < length(theSize)
theSubs{end+1} = s;
end

% Note: We compute a base-1 surrogate of theSubs,
% in order to keep the pre-allocated "result" matrix
% as small as possible.

subs = cell(size(theSubs)); %Aqui me marca el error
siz = zeros(size(subs));
for i = 1:length(theSubs)
if isequal(theSubs{i}, ':')
theSubs{i} = 1:theSize(i);
end
subs{i} = theSubs{i} - min(theSubs{i}) + 1; % Base-1.
siz(i) = max(subs{i});
end

result = zeros(siz); % Pre-allocate.

for j = 1:length(theVars)
% [from, to] = mapsubs(theSrcsubs{j}, theDstsubs{j}, theSubs);
[from, to] = mapsubs(theSrcsubs{j}, theDstsubs{j}, subs);
if ~isempty(from) & ~isempty(to)
x = ncsubsref(theVars{j}, '()', from);
result(to{:}) = x;
end
end

% result = result(theSubs{:}); % Subset.

result = result(subs{:}); % Subset.

if nargout > 0
theResult = result;
else
disp(result)
end
return
end

% Regular processing.

result = [];
if nargout > 0, theResult = result; end

s = theStruct;
theType = s(1).type;
theSubs = s(1).subs;
s(1) = [];

nccheck(self)
theAutoscaleflag = (autoscale(self) == 1);
theDatatype = datatype(self);
theTypelen = ncmex('typelen', theDatatype);
isUnsigned = unsigned(self);
theFillvalue = fillval(self);
theAutonanflag = (autonan(self) == 1) & ~isempty(theFillvalue);
if theAutoscaleflag
theScalefactor = scalefactor(self);
theAddoffset = addoffset(self);
end

switch theType
case '()' % Variable data by index: self(..., ...).
indices = theSubs;
theSize = ncsize(self);
for i = 1:length(indices)
if isa(indices{i}, 'double')
if any(diff(diff(indices{i})))
disp(' ## Indexing strides must be positive and constant.')
return
end
end
end

% Flip and permute indices before proceeding,
% since we are using virtual indexing.

theOrientation = orient(self);
if any(theOrientation < 0) | any(diff(theOrientation) ~= 1)
for i = 1:length(theOrientation)
if theOrientation(i) < 0
if isa(indices{i}, 'double') % Slide the indices.
indices{i} = fliplr(theSize(i) + 1 - indices{i});
end
end
end
indices(abs(theOrientation)) = indices;
theSize(abs(theOrientation)) = theSize;
end

if prod(theSize) > 0
start = zeros(1, length(theSize));
count = ones(1, length(theSize));
stride = ones(1, length(theSize));
for i = 1:min(length(indices), length(theSize))
k = indices{i};
if ~isstr(k) & ~strcmp(k, ':') & ~strcmp(k, '-')
start(i) = k(1)-1;
count(i) = length(k);
d = 0;
if length(k) > 1, d = diff(k); end
stride(i) = max(d(1), 1);
else
count(i) = -1;
if i == length(indices) & i < length(theSize)
j = i+1:length(theSize);
count(j) = -ones(1, length(j));
end
end
end
start(start < 0) = 0;
stride(stride < 0) = 1;
for i = 1:length(count)
if count(i) == -1
maxcount = fix((theSize(i)-start(i)+stride(i)-1) ./ stride(i));
count(i) = maxcount;
end
end
theNetCDF = parent(self);
theNetCDF = endef(theNetCDF);
count(count < 0) = 0;
if any(count == 0), error(' ## Bad count.'), end
if all(count == 1)
[result, status] = ncmex('varget1', ncid(self), varid(self), ...
start, 0);

elseif all(stride == 1)

[result, status] = ncmex('varget', ncid(self), varid(self), ...
start, count, 0);
else
imap = [];
[result, status] = ncmex('vargetg', ncid(self), varid(self), ...
start, count, stride, imap, ...
0);
end
if theAutonanflag & status >= 0
f = find(result == theFillvalue);
if any(f), result(f) = NaN; end
end
if theAutoscaleflag & status >= 0
result = result .* theScalefactor + theAddoffset;
end
if isUnsigned & prod(size(result)) > 0
result(result < 0) = 2^(8*theTypelen) + result(result < 0);
end
else
result = [];
status = 0;
end
if status >= 0 & prod(size(result)) > 0
result = permute(result, length(size(result)):-1:1);
theOrientation = orient(self);
if any(theOrientation < 0) | any(diff(theOrientation) ~= 1)
for i = 1:length(theOrientation)
if theOrientation(i) < 0
result = flipdim(result, abs(theOrientation(i)));
end
end
if length(theOrientation) < 2
theOrientation = [theOrientation 2];
end
result = permute(result, abs(theOrientation));
end
elseif status >= 0 & prod(size(result)) == 0
result = [];
else
status, prod_size_result = prod(size(result)) % ***
warning(' ## ncvar/subsref failure.')
end
case '.' % Attribute: self.theAttname(...)
theAttname = theSubs;
while length(s) > 0 % Dotted name.
switch s(1).type
case '.'
theAttname = [theAttname '.' s(1).subs];
s(1) = [];
otherwise
break
end
end
result = att(self, theAttname);
if ~isempty(result), result = subsref(result, s); end
otherwise
warning([' ## Illegal syntax: "' theType '"'])
end

if nargout > 0 % Always true.
theResult = result;
else % Is there any way to force this?
c = ncatt('C_format', self);
if ~isempty(c)
c = c(:);
s = size(result)
result = result.';
result = result(:);
step = prod(s)/s(1);
k = 1:step;
for i = 1:s(1)
fprintf(c, result(k));
fprintf('\n');
k = k + step;
end
else
disp(result)
end
end
================================================

Si alguien sabe como solucionar este error, se los agradecería pues esto es parte de un trabajo que me urge sacar y ya tengo el tiempo encima.

[AlvaroG]

Pues si te dice que una variable no está inicializada, ya se trata de un problema de tu programa MatLab, no de Linux.
Siendo este un foro de Linux, no necesariamente vas a encontrar gente que te pueda ayudar con problemas de MatLab...


Saludos.

[Gamz]

Hola a todos yo también estoy intentando correr el modelo ROMS pero en Ubuntu al compilar jobcomp tengo el siguiente error:
>> ./jobcomp
cp: No match.
cp: No match.
OPERATING SYSTEM IS: Linux
/bin/rm -rf core *.o AGRIFZOOM/AGRIF_YOURFILES/*.o *.i *.s *.f *.trace *.mod
/bin/rm -rf roms mpc cross_matrix cppcheck srcscheck checkkwds partit ncjoin ncrename ./rii_files
/opt/intel/fc/10.1.021/bin/fpp -free -P -I../netcdf_ifc/ -I/home/gamz/include mpc.F > mpc.f
mpc.F(124): #warning: keyword redefined: integer
ifort -O3 -w90 -w95 -cm -72 -fno-alias -i4 -r8 -Vaxlib -o mpc mpc.f
make: ifort: Command not found
make: *** [mpc] Error 127
/opt/intel/fc/10.1.021/bin/fpp -free -P -I../netcdf_ifc/ -I/home/tavo/include main.F | ./mpc > main.f
/bin/sh: ./mpc: not found
make: *** [main.o] Error 127
mv: cannot stat `roms': No such file or directory

Alguien tiene idea como corregir el error, saludos.

[AlvaroG]

Hola Gamz, bienvenido a forosdelweb.
Te recomiendo leer este mensaje, simplemente para que puedas disfrutar de una buena estadía por acá.

Contestando a tu pregunta, en el mensaje de error podés ver que el sistema no puede encontrar el archivo ifort. El segundo error es que no puede encontrar mpc, pero si ves con cuidado es ifort el que debe crear a mpc.

Una búsqueda por ifort me devuelve esto, que seguramente tengas que instalar:
http://www.intel.com/cd/software/pro...eng/282048.htm


Saludos y suerte